Hi, I have now fixed the bug in the main 1.3 line. The problem was that the variable 'ds.relax_gui.sequencefile' did not exist, it had been renamed. So I have used your data and successfully calculated the R2 values. I was wondering if it would be ok to add your truncated data to the relax test suite so that I could be sure that such a bug never returns? It would be much appreciated.
One issue still is that the GUI is not very flexible and you cannot currently specify which columns of your sequence file correspond to residue names, residue numbers, spin numbers, etc. It is hardcoded to assume that a residue is in the first column :S The prompt/scripting based interface does not have this problem and you can have your sequence data in any format. This is one of the reasons why I am currently rewriting the entire GUI - to eliminate such undocumented inflexibilities. For the new design you will have to wait. Unfortunately it will also take me a while before I can release a new version of relax. However if you would like to use the fixed code, you could follow the instructions at http://www.nmr-relax.com/download.html#Source_code_repository. Note for the R1 and R2, you will need to have the python development libraries installed and the scons program (as well as a C compiler). See the instructions at http://www.nmr-relax.com/download.html#Source_code_release. If this is not possible and you cannot wait, you could try the relax_fit.py sample script (in the sample_script directory) and run this from the command line. Regards, Edward On 27 June 2011 12:44, Aldino <[email protected]> wrote: > Dear Edward, > > I ran relax -g --debug and I got the following: > > > File "/home/aldino/Software/relax-1.3.10/gui/analyses/auto_rx_base.py", > line 438, in execute > self.execute_thread('dummy') > File "/home/aldino/Software/relax-1.3.10/gui/analyses/auto_rx_base.py", > line 463, in execute_thread > data, complete, missing = self.assemble_data() > File "/home/aldino/Software/relax-1.3.10/gui/analyses/auto_rx_base.py", > line 288, in assemble_data > data.seq_args = [ds.relax_gui.sequencefile, None, None, 1, None, None, > None, None] > AttributeError: 'Gui' object has no attribute 'sequencefile' > > It seems that it has some problem with the sequence.... > > the file I am using is of the type (*.seq): > > MET 1 > ALA 2 > SER 3 > ALA 4 > ... > > and it works for the NOE calculation... > In the meanwile I am writing the bug report. > > Cheers, > Aldino > > > > > -----Mensagem Original----- From: Edward d'Auvergne > Sent: Monday, June 27, 2011 10:08 AM > To: Aldino > Cc: [email protected] > Subject: Re: R1 and R2 calculation error > > Hi, > > Thank you for the information. I've been looking into this problem, > but it is hard to diagnose. There has been a bug triggered somewhere > in the setup of the data (I think) but as this is running in a thread, > the relax error message is not being caught and reported. That is the > meaning of "Unhandled exception in thread". So the real cause is > lost. There is a way of bypassing this by using the debug flag. I.e. > running relax as: > > $ relax -g --debug > > This will cause the real source of the error to be printed in the > terminal/shell in which you launched relax. It would be very useful > if you were to report this in a bug report though, including a tiny, > randomised data set which still triggers the bug > (https://gna.org/bugs/?func=additem&group=relax). Having the data > will allow me to very quickly reproduce the bug and hopefully have a > fix within ~5 min. > > Cheers, > > Edward > > > > On 27 June 2011 10:39, Aldino <[email protected]> wrote: >> >> Dear Edward, >> >> once again, thank you for your reply. This time I´ll make sure the message >> goes to the mailing list. >> So, here it goes: >> >> I am using the latest Relax version (3.1.10) >> >> Below I send the relax info (also in attach): >> >> relax 1.3.10 >> >> Molecular dynamics by NMR data analysis >> >> Copyright (C) 2001-2006 Edward d'Auvergne >> Copyright (C) 2006-2011 the relax development team >> >> This is free software which you are welcome to modify and redistribute >> under >> the conditions of the >> GNU General Public License (GPL). This program, including all modules, is >> licensed under the GPL >> and comes with absolutely no warranty. For details type 'GPL' within the >> relax prompt. >> >> Assistance in using the relax prompt and scripting interface can be >> accessed >> by typing 'help' within >> the prompt. >> >> Hardware information: >> Machine: i686 >> Processor: i686 >> >> System information: >> System: Linux >> Release: 2.6.38-8-generic >> Version: #42-Ubuntu SMP Mon Apr 11 03:31:50 UTC 2011 >> GNU/Linux version: Ubuntu 11.04 natty >> Distribution: Ubuntu 11.04 natty >> Full platform string: >> Linux-2.6.38-8-generic-i686-with-Ubuntu-11.04-natty >> >> Software information: >> Architecture: 32bit ELF >> Python version: 2.7.1+ >> Python branch: tags/r271 >> Python build: r271:86832, Apr 11 2011 18:05:24 >> Python compiler: GCC 4.5.2 >> Python implementation: CPython >> Python revision: 86832 >> Numpy version: 1.5.1 >> Libc version: glibc 2.4 >> >> Python packages (most are optional): >> >> Package Installed Version Path >> minfx True Unknown >> /home/aldino/Software/relax-1.3.10/minfx >> bmrblib False >> numpy True 1.5.1 >> /usr/lib/pymodules/python2.7/numpy >> ScientificPython True 2.8 >> /usr/lib/python2.7/dist-packages/Scientific >> wxPython True >> mpi4py False >> epydoc False >> optparse True 1.5.3 >> /usr/lib/python2.7/optparse.pyc >> Numeric False >> readline True >> /usr/lib/python2.7/lib-dynload/readline.so >> profile True >> /usr/lib/python2.7/profile.pyc >> bz2 True >> /usr/lib/python2.7/lib-dynload/bz2.so >> gzip True >> /usr/lib/python2.7/gzip.pyc >> os.devnull True >> /usr/lib/python2.7/os.pyc >> >> Compiled relax C modules: >> Relaxation curve fitting: True >> >> >> In the mean wile I will try to submit a bug report for this. >> >> Thanks, >> Aldino >> >> -----Mensagem Original----- From: Edward d'Auvergne >> Sent: Wednesday, June 22, 2011 3:35 PM >> To: Aldino >> Cc: [email protected] >> Subject: Re: R1 and R2 calculation error >> >> Dear Aldino, >> >> Welcome to the relax mailing lists. The problem you are seeing could >> possibly be related to an older version of relax. Which version are >> you using? Could you copy and paste the output of: >> >> $ relax --info >> >> If you are using version 1.3.9 or earlier, I would recommend trying >> out 1.3.10 and see if the problem is solved. If you are using version >> 1.3.10, you have encountered a new bug. If so, would you be able to >> submit a bug report for this? See >> https://gna.org/bugs/?func=additem&group=relax. I would recommend >> including a minimal data set (only data for one or two spins, >> randomised if you would like to keep it private) and instructions for >> how to trigger the bug. >> >> Cheers, >> >> Edward >> >> >> >> On 21 June 2011 18:05, Aldino <[email protected]> wrote: >>> >>> Hi! >>> >>> I have just started using RelaxGUI and I’m having some problems when >>> trying >>> to calculate R1 and R2. >>> >>> For the steady-state NOE everything is alright but when I start the R1 >>> calculation I get: >>> >>> >>> >>> “Starting R1 calculation >>> >>> Unhandled exception in thread started by <bound method >>> Auto_r1.execute_thread of <gui.analyses.auto_r1.Auto_r1 instance at >>> 0xa47556c>>” >>> >>> >>> >>> The same thing when trying to calculate R2... >>> >>> >>> >>> “Starting R2 calculation >>> >>> Unhandled exception in thread started by <bound method >>> Auto_r2.execute_thread of <gui.analyses.auto_r2.Auto_r2 instance at >>> 0xa46f4cc>>” >>> >>> >>> >>> Please help... >>> Thanks, >>> Aldino >>> >>> >>> >>> ______________________________________________ >>> Aldino Viegas, PhD Student >>> Dep. Química, REQUIMTE >>> Faculdade de Ciências e Tecnologia >>> Universidade Nova de Lisboa >>> 2829-516 Caparica, Portugal >>> >>> Tlf. +351 212948300 >>> Ext. 10900 Lab. 106-A >>> [email protected] >>> _______________________________________________ >>> relax (http://nmr-relax.com) >>> >>> This is the relax-users mailing list >>> [email protected] >>> >>> To unsubscribe from this list, get a password >>> reminder, or change your subscription options, >>> visit the list information page at >>> https://mail.gna.org/listinfo/relax-users >>> >>> >> > > _______________________________________________ relax (http://nmr-relax.com) This is the relax-users mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-users
